Input: Metadata bacteria: Database_MRB_isolates & database_raw, Mapping results: Mapping in 4 soils and feedback, Phylogeny: Tree compouted from 16s sequences
Phylogeny without tree using radialNetwork()
Abundance of isolates from strain collection in microbiome datasets of the field & greenhouse Form quantitative values to quantitative. Abundant strains are defined as abundance > 0.1.
The tree is annotated with the quantitative abundance data from mapping greenhouse root microbiome dataset and qualitative information on the abundance in field microbiome datasets in the field (Changins, Zurich, Ithaca) and in the greenhouse (Sheffield). The outermost ring indicates the strains used in growth assays.
Abundance AMPO strains
| Location_Background | Experiment | Family | Abundance_mean |
|---|---|---|---|
| Changins_B73 | field | Sphingomonadaceae | 0.6158494 |
| Greenhouse_B73 | feedback | Sphingomonadaceae | 5.4337948 |
| Reckenholz_B73 | field | Sphingomonadaceae | 1.0963679 |
| Aurora_W22 | field | Sphingomonadaceae | 3.2212013 |
| Changins_B73 | field | Rhizobiaceae | 0.4031122 |
| Greenhouse_B73 | feedback | Rhizobiaceae | 1.6348278 |
| Reckenholz_B73 | field | Rhizobiaceae | 0.9226987 |
| Aurora_W22 | field | Rhizobiaceae | 0.7081318 |
| Changins_B73 | field | Moraxellaceae | 0.0000000 |
| Reckenholz_B73 | field | Moraxellaceae | 0.0000000 |
| Aurora_W22 | field | Moraxellaceae | 0.0075401 |
| Changins_B73 | field | Micrococcaceae | 0.2421541 |
| Greenhouse_B73 | feedback | Micrococcaceae | 0.1630430 |
| Reckenholz_B73 | field | Micrococcaceae | 0.3605178 |
| Aurora_W22 | field | Micrococcaceae | 0.2343906 |
| Changins_B73 | field | Microbacteriaceae | 0.4527121 |
| Greenhouse_B73 | feedback | Microbacteriaceae | 1.0564132 |
| Reckenholz_B73 | field | Microbacteriaceae | 1.0495033 |
| Aurora_W22 | field | Microbacteriaceae | 0.5498872 |
| Changins_B73 | field | Enterobacteriaceae | 1.2469469 |
| Greenhouse_B73 | feedback | Enterobacteriaceae | 0.7758565 |
| Reckenholz_B73 | field | Enterobacteriaceae | 11.5794241 |
| Aurora_W22 | field | Enterobacteriaceae | 2.0172681 |
| Location_Background | Experiment | Abundance_sum |
|---|---|---|
| Changins_B73 | field | 2.960775 |
| Greenhouse_B73 | feedback | 9.063935 |
| Reckenholz_B73 | field | 15.008512 |
| Aurora_W22 | field | 6.738419 |
sessionInfo()
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.3.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: Europe/Zurich
## tzcode source: internal
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] Cairo_1.6-0 networkD3_0.4 data.tree_1.0.0 ggnewscale_0.4.9
## [5] ggsci_3.0.0 wesanderson_0.3.6 ggtree_3.8.0 ape_5.7-1
## [9] reshape2_1.4.4 ggdendro_0.1.23 pheatmap_1.0.12 RColorBrewer_1.1-3
## [13] tibble_3.2.1 pander_0.6.5 ggpmisc_0.5.4-1 ggpp_0.5.4
## [17] forcats_1.0.0 stringr_1.5.0 readr_2.1.4 tidyr_1.3.0
## [21] readxl_1.4.2 ggplot2_3.4.3 magrittr_2.0.3 dplyr_1.1.2
## [25] plyr_1.8.8
##
## loaded via a namespace (and not attached):
## [1] gtable_0.3.4 xfun_0.39 bslib_0.5.0 htmlwidgets_1.6.2
## [5] lattice_0.21-8 tzdb_0.4.0 yulab.utils_0.0.6 vctrs_0.6.3
## [9] tools_4.3.1 generics_0.1.3 parallel_4.3.1 fansi_1.0.4
## [13] highr_0.10 pkgconfig_2.0.3 Matrix_1.5-4.1 ggplotify_0.1.0
## [17] lifecycle_1.0.3 farver_2.1.1 compiler_4.3.1 treeio_1.24.1
## [21] MatrixModels_0.5-1 munsell_0.5.0 SparseM_1.81 ggfun_0.1.0
## [25] quantreg_5.95 htmltools_0.5.5 sass_0.4.6 lazyeval_0.2.2
## [29] yaml_2.3.7 pillar_1.9.0 jquerylib_0.1.4 ellipsis_0.3.2
## [33] MASS_7.3-60 cachem_1.0.8 nlme_3.1-162 tidyselect_1.2.0
## [37] aplot_0.1.10 digest_0.6.31 stringi_1.7.12 purrr_1.0.1
## [41] labeling_0.4.2 splines_4.3.1 fastmap_1.1.1 colorspace_2.1-0
## [45] cli_3.6.1 patchwork_1.1.2 survival_3.5-5 utf8_1.2.3
## [49] withr_2.5.0 scales_1.2.1 rmarkdown_2.22 igraph_1.5.0
## [53] cellranger_1.1.0 hms_1.1.3 evaluate_0.21 knitr_1.43
## [57] gridGraphics_0.5-1 rlang_1.1.1 Rcpp_1.0.11 tidytree_0.4.2
## [61] glue_1.6.2 polynom_1.4-1 rstudioapi_0.14 jsonlite_1.8.5
## [65] R6_2.5.1